ruanjue/smartdenovo

how to adjusting parameters to improve the assembly result

linshengnan2020 opened this issue · 3 comments

linshengnan2020 commented

hi, I have run a 1G , diploid genome with 70~80% repetitive sequences genome . The coverage of my PacBio data is approximately 40 x. As a result the final assembly N50 is 82k . I would be interested how to adjust the parameters to improve the assembly result. Could you please give me some advises? Thank you very much!

ruanjue commented

Try other assemblers first, if all give small N50, let us discuss it again.

linshengnan2020 commented

I have used several assemblers ，such as mecat2, flye, WTDBG2, smartdenovo and nextdenovo , the results of smartdenovo and nextdenovo were relatively good, the N50 is 82k and 157k.

ruanjue commented

Have a look at smartdenovo.pl, have you chosen the zmo engine? The default is dmo, much faster, but gives reletively worse alignments.